SMTL ID : 9rmw.1

GluA4 in complex with TARP-2, open state, structure of TMD/LBD domains

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

18 x PLM: PALMITIC ACID(Covalent)(Non-covalent)

PLM.1: 7 residues within 4Å: Chain A: M.809, L.810, L.813, C.817 Chain C: S.144, L.147 Ligands: PLM.5 Ligand excluded by PLIP PLM.2: 7 residues within 4Å: Chain A: V.516, F.517, Y.799, G.804 Chain G: I.602, V.606 Ligands: PLM.13 Ligand excluded by PLIP PLM.5: 7 residues within 4Å: Chain A: C.817 Chain C: L.114, S.137, I.140, F.141, S.144 Ligands: PLM.1 Ligand excluded by PLIP PLM.7: 7 residues within 4Å: Chain B: G.806, L.813, C.817 Chain H: S.144, S.148 Ligands: PLM.9, PLM.29 Ligand excluded by PLIP PLM.8: 4 residues within 4Å: Chain B: V.516 Chain H: F.97 Ligands: PLM.12, PLM.29 Ligand excluded by PLIP PLM.9: 8 residues within 4Å: Chain B: L.813, C.817, S.820 Chain H: S.137, I.140, F.141, S.144 Ligands: PLM.7 Ligand excluded by PLIP PLM.12: 4 residues within 4Å: Chain B: F.517, I.800 Ligands: OLC.3, PLM.8 Ligand excluded by PLIP PLM.13: 7 residues within 4Å: Chain A: Y.799 Chain C: A.94, F.97, L.98, F.107, I.151 Ligands: PLM.2 Ligand excluded by PLIP PLM.14: 8 residues within 4Å: Chain D: A.94, F.97, L.98, F.107 Chain G: Y.799, V.802 Ligands: PLM.22, PLM.25 Ligand excluded by PLIP PLM.15: 7 residues within 4Å: Chain E: L.110, S.137, I.140, F.141, S.144 Chain F: C.817 Ligands: PLM.16 Ligand excluded by PLIP PLM.16: 7 residues within 4Å: Chain E: L.147, S.148 Chain F: M.809, L.810, L.813, C.817 Ligands: PLM.15 Ligand excluded by PLIP PLM.17: 9 residues within 4Å: Chain E: A.94, F.97, L.98, F.107, I.151 Chain F: V.516, Y.799, G.803 Ligands: PLM.18 Ligand excluded by PLIP PLM.18: 8 residues within 4Å: Chain B: V.606 Chain F: V.516, F.517, Y.799, I.800, G.804, L.807 Ligands: PLM.17 Ligand excluded by PLIP PLM.22: 7 residues within 4Å: Chain D: S.144, S.148 Chain G: G.806, L.813, C.817 Ligands: PLM.14, PLM.26 Ligand excluded by PLIP PLM.24: 4 residues within 4Å: Chain G: F.517, I.800 Ligands: OLC.23, PLM.25 Ligand excluded by PLIP PLM.25: 7 residues within 4Å: Chain D: A.94 Chain F: V.606 Chain G: V.516, G.804, L.807 Ligands: PLM.14, PLM.24 Ligand excluded by PLIP PLM.26: 7 residues within 4Å: Chain D: S.137, I.140, F.141, S.144 Chain G: F.816, S.820 Ligands: PLM.22 Ligand excluded by PLIP PLM.29: 7 residues within 4Å: Chain B: Y.799, V.802 Chain H: A.94, F.97, L.98 Ligands: PLM.7, PLM.8 Ligand excluded by PLIP

2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.3: 7 residues within 4Å: Chain A: L.598, R.601 Chain B: Y.535, F.576, L.583, F.586 Ligands: PLM.12 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.535, B:Y.535, B:Y.535, B:F.576, B:L.583, B:F.586, A:R.601 Hydrogen bonds: A:L.598 OLC.23: 7 residues within 4Å: Chain F: L.598, R.601 Chain G: Y.535, F.576, L.583, F.586 Ligands: PLM.24 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:Y.535, G:Y.535, G:Y.535, G:F.576, G:L.583, G:F.586, F:R.601

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.4: 14 residues within 4Å: Chain A: K.495, P.496, M.498, S.499, L.753, S.756, L.761, D.762, K.765 Chain G: I.483, P.496, S.731, K.732, G.733 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: A:K.495, A:P.496, A:L.753, G:I.483, G:I.483, G:I.483, G:P.496, G:K.732 Hydrogen bonds: A:M.498, A:S.499, A:S.756, A:S.756, A:K.765, G:S.731, G:S.731 CYZ.11: 14 residues within 4Å: Chain B: P.496, F.497, M.498, S.499, L.753, S.756, L.761, D.762, K.765 Chain F: I.483, S.499, S.731, K.732, G.733 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:L.753, B:L.761, F:I.483, F:K.732 Hydrogen bonds: B:S.499, B:S.499, B:S.756, B:S.756, F:S.731 CYZ.19: 13 residues within 4Å: Chain B: I.483, S.731, K.732, G.733 Chain F: K.495, P.496, F.497, M.498, S.499, L.753, L.761, D.762, K.765 11 PLIP interactions: 5 interactions with chain F, 6 interactions with chain B Hydrophobic interactions: F:K.495, F:P.496, F:L.753, B:I.483, B:I.483, B:I.483, B:K.732 Hydrogen bonds: F:S.499, F:K.765, B:S.731, B:S.731 CYZ.28: 13 residues within 4Å: Chain A: I.483, S.731, K.732, G.733 Chain G: P.496, F.497, M.498, S.499, L.753, S.756, L.761, D.762, K.765 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain G Hydrophobic interactions: A:I.483, A:I.483, A:K.732, G:L.753, G:L.761 Hydrogen bonds: A:S.731, G:S.499, G:S.499, G:S.756, G:S.756

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.6: 11 residues within 4Å: Chain A: Y.452, P.480, L.481, T.482, R.487, L.652, G.655, S.656, T.657, E.707, M.710 8 PLIP interactions: 8 interactions with chain A, Hydrogen bonds: A:P.480, A:T.482, A:T.482, A:T.482, A:S.656, A:T.657, A:T.657 Salt bridges: A:R.487 GLU.10: 11 residues within 4Å: Chain B: Y.452, P.480, L.481, T.482, R.487, L.652, G.655, S.656, T.657, E.707, Y.734 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.452, B:Y.452 Hydrogen bonds: B:P.480, B:T.482, B:T.482, B:S.656, B:T.657, B:T.657, B:E.707, E.10 Salt bridges: B:R.487 GLU.21: 10 residues within 4Å: Chain F: Y.452, P.480, L.481, T.482, R.487, L.652, G.655, S.656, T.657, E.707 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:Y.452, F:L.652 Hydrogen bonds: F:T.482, F:T.482, F:T.482, F:T.482, F:S.656, F:T.657, F:T.657 Salt bridges: F:R.487 GLU.27: 11 residues within 4Å: Chain G: Y.452, P.480, L.481, T.482, R.487, L.652, S.656, T.657, L.706, E.707, Y.734 11 PLIP interactions: 10 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: G:Y.452, G:E.707 Hydrogen bonds: G:P.480, G:T.482, G:T.482, G:S.656, G:T.657, G:E.707, G:E.707, E.27 Salt bridges: G:R.487

1 x CA: CALCIUM ION(Non-functional Binders)

CA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vega-Gutierrez, C. et al., GluA4 AMPA receptor gating mechanisms and modulation by auxiliary subunits. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-09-24

Peptides

Isoform 2 of Glutamate receptor 4: ABFG
Voltage-dependent calcium channel gamma-2 subunit: CDEH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
C

G
D

C
E

D
F

E
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Glutamate receptor 4

Voltage-dependent calcium channel gamma-2 subunit

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